The influence of the rumen microbiome on feed efficiency and methane yield - a taxonomic and functional approach

Abstract

The rumen microbiome plays a fundamental role in the digestion of plant biomass, and differences in the taxonomic and functional composition of these microorganisms have been demonstrated to influence feed efficiency and methane production. However, the results are not consistent across the studies, and the microbial taxa and the metabolic pathways related to the feed efficiency phenotype and the methane production are not fully elucidated. Additionally, all the studies that explored the relationship between the rumen microbiome and these traits were developed in cattle raised in temperate areas. Section 1 is a review that aimed to discuss how the rumen parameters – and the rumen as a whole – are related to feed efficiency. The rumen is a complex environment and the rumen parameters influence each other, however, most studies do not consider these interactions and discuss the rumen parameters separately. Section 2 compared all the studies published about the relationship between rumen microbiome and residual feed intake (RFI) in order to investigate the influence of the variables of the study and the methodology used (e.g., animal breed, diet, sequencing platform and hypervariable region used on the sequencing) on the microbial data registered. On Section 3 and Section 4 was used Illumina sequencing of the 16S and 18S rRNA in order to explore the taxonomic and functional composition of the rumen microbiome related to feed efficiency and methane yield. These are the first studies to explore the relationship between the rumen microorganisms and these traits in cattle raised under tropical conditions. Advances in omics technologies in the last years have allowed a better exploration of complex microbial communities, such as the rumen. This thesis demonstrates the importance of the meta-omics technologies in order to better understand the rumen microbiome and its relationship with feed efficiency and methane production.